add parameters to model_configure

[ghost]

model_configure is currently mostly hardcoded; need to add parameters to the ModelConfiguration object:

nemspy/nemspy/configuration.py

Lines 373 to 528 in f0b9c25

	class ModelConfigurationFile(ConfigurationFile):
	name = 'model_configure'
	def __init__(self, start_time: datetime, duration: timedelta, sequence: RunSequence):
	self.start_time = start_time
	self.duration = duration
	super().__init__(sequence)
	def write(self, directory: PathLike, overwrite: bool = False):
	directory = ensure_directory(directory)
	filename = directory / self.name
	if filename.exists():
	LOGGER.warning(
	f'{"overwriting" if overwrite else "skipping"} ' f'existing file "{filename}"'
	)
	if not filename.exists() or overwrite:
	LOGGER.debug(f'writing model configuration to "{filename}"')
	with open(filename, 'w') as output_file:
	output_file.write(str(self))
	symbolic_link_filename = directory / 'atm_namelist.rc'
	try:
	symbolic_link_filename.symlink_to(filename)
	except Exception as error:
	LOGGER.warning(f'could not create symbolic link: {error}')
	with open(symbolic_link_filename, 'w') as output_file:
	output_file.write(str(self))
	def __str__(self) -> str:
	duration_hours = round(self.duration / timedelta(hours=1))
	return '\n'.join(
	[
	'core: gfs',
	'print_esmf: .true.',
	'',
	'nhours_dfini=0',
	'',
	'#nam_atm +++++++++++++++++++++++++++',
	'nlunit: 35',
	'deltim: 900.0',
	'fhrot: 0',
	'namelist: atm_namelist',
	'total_member: 1',
	'grib_input: 0',
	f'PE_MEMBER01: {self.sequence.processors}',
	'PE_MEMBER02',
	'PE_MEMBER03',
	'PE_MEMBER04',
	'PE_MEMBER05',
	'PE_MEMBER06',
	'PE_MEMBER07',
	'PE_MEMBER08',
	'PE_MEMBER09',
	'PE_MEMBER10',
	'PE_MEMBER11',
	'PE_MEMBER12',
	'PE_MEMBER13',
	'PE_MEMBER14',
	'PE_MEMBER15',
	'PE_MEMBER16',
	'PE_MEMBER17',
	'PE_MEMBER18',
	'PE_MEMBER19:',
	'PE_MEMBER20:',
	'PE_MEMBER21:',
	'',
	'# For stochastic perturbed runs - added by Dhou and Wyang',
	'--------------------------------------------------------',
	'# ENS_SPS, logical control for application of stochastic '
	'perturbation scheme',
	'# HH_START, start hour of forecast, and modified ' 'ADVANCECOUNT_SETUP',
	'# HH_INCREASE and HH_FINAL are fcst hour increment and end '
	'hour of forecast',
	'# ADVANCECOUNT_SETUP is an integer indicating the number of '
	'time steps between integration_start and the time when model '
	'state is saved for the _ini of the GEFS_Coupling, currently is '
	'0h.',
	'',
	'HH_INCREASE: 600',
	'HH_FINAL: 600',
	'HH_START: 0',
	'ADVANCECOUNT_SETUP: 0',
	'',
	'ENS_SPS: .false.',
	'HOUTASPS: 10000',
	'',
	'#ESMF_State_Namelist +++++++++++++++',
	'',
	'RUN_CONTINUE: .false.',
	'',
	'#',
	'dt_int: 900',
	'dt_num: 0',
	'dt_den: 1',
	f'start_year: {self.start_time.year}',
	f'start_month: {self.start_time.month}',
	f'start_day: {self.start_time.day}',
	f'start_hour: {self.start_time.hour}',
	f'start_minute: {self.start_time.minute}',
	f'start_second: {self.start_time.second}',
	f'nhours_fcst: {duration_hours:.0f}',
	'restart: .false.',
	f'nhours_fcst1: {duration_hours:.0f}',
	'im: 192',
	'jm: 94',
	'global: .true.',
	'nhours_dfini: 0',
	'adiabatic: .false.',
	'lsoil: 4',
	'passive_tracer: .true.',
	'dfilevs: 64',
	'ldfiflto: .true.',
	'num_tracers: 3',
	'ldfi_grd: .false.',
	'lwrtgrdcmp: .false.',
	'nemsio_in: .false.',
	'',
	'',
	'#jwstart added quilt',
	'###############################',
	'#### Specify the I/O tasks ####',
	'###############################',
	'',
	'',
	'quilting: .false. #For asynchronous '
	'quilting/history writes',
	'read_groups: 0',
	'read_tasks_per_group: 0',
	'write_groups: 1',
	'write_tasks_per_group: 3',
	'',
	'num_file: 3 #',
	"filename_base: 'SIG.F' 'SFC.F' 'FLX.F'",
	"file_io_form: 'bin4' 'bin4' 'bin4'",
	"file_io: 'DEFERRED' 'DEFERRED' 'DEFERRED' " "'DEFERRED' #",
	'write_dopost: .false. # True--> run do on ' 'quilt',
	'post_gribversion: grib1 # True--> grib version for '
	'post output files',
	'gocart_aer2post: .false.',
	'write_nemsioflag: .TRUE. # True--> Write nemsio '
	'run history files',
	'nfhout: 3',
	'nfhout_hf: 1',
	'nfhmax_hf: 0',
	'nsout: 0',
	'',
	'io_recl: 100',
	"io_position: ' '",
	"io_action: 'WRITE'",
	"io_delim: ' '",
	"io_pad: ' '",
	'',
	'#jwend',
	]
	)

[ghost]

this template might be useful:
https://github.com/NOAA-EMC/DATM-MOM6-CICE5/blob/ca3d21bd89f967e4c25953eaa3349829c739b528/parm/model_configure.IN#L1-L22

total_member:            1 
print_esmf:              .true.
PE_MEMBER01:             @[TASKS]
start_year:              @[SYEAR]
start_month:             @[SMONTH]
start_day:               @[SDAY]
start_hour:              @[SHOUR]
start_minute:            0
start_second:            0
nhours_fcst:             @[FHMAX]
RUN_CONTINUE:            .false.
ENS_SPS:                 .false.

dt_atmos:                   @[DT_ATMOS]
atm_coupling_interval_sec:  @[coupling_interval_fast_sec]

iatm: @[IATM]
jatm: @[JATM]

cdate0: @[CDATE]
nfhout: @[NFHOUT]
filename_base: @[FILENAME_BASE]

[ghost]

only these variables are required in model_configure:
https://github.com/saeed-moghimi-noaa/cpl_tools/blob/4772824d21bd4e79f915a0932315fb627b6186be/01_prep/01_cpl_run_dir/00-prepare-nsemodel-run.py#L256-L264